Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate 3606894 Dshi_0324 acetylglutamate kinase (RefSeq)
Query= BRENDA::Q9HTN2 (301 letters) >FitnessBrowser__Dino:3606894 Length = 287 Score = 288 bits (736), Expect = 1e-82 Identities = 149/291 (51%), Positives = 198/291 (68%), Gaps = 13/291 (4%) Query: 5 RDDAAQVAKVLSEALPYIRRFVGKTLVIKYGGNAMESEELKAGFARDVVLMKAVGINPVV 64 + D A+ LSEA+P++RR+ +VIK+GG+AM E A FARD+VLM+ VG+NPV+ Sbjct: 7 KSDWIATARTLSEAVPFLRRYDDAIVVIKFGGHAMGDAEAMASFARDIVLMRQVGVNPVI 66 Query: 65 VHGGGPQIGDLLKRLSIESHFIDGMRVTDAATMDVVEMVLGGQVNKDIVNLINRHGGSAI 124 VHGGGP I +L +L I S F++G RVTDAAT++VVEMVL G VNK IV INR GG AI Sbjct: 67 VHGGGPMINAMLAKLDINSDFVNGKRVTDAATIEVVEMVLSGLVNKRIVQAINREGGRAI 126 Query: 125 GLTGKDAELIRAKKLTVTRQTPEMTKPEIIDIGHVGEVTGVNVGLLNMLVKGDFIPVIAP 184 GL+GKDA LI + P +G VGE V L LV+ + IPVIAP Sbjct: 127 GLSGKDANLI-------------VCDPADPALGFVGEPVEVTPDTLLQLVRSEIIPVIAP 173 Query: 185 IGVGSNGESYNINADLVAGKVAEALKAEKLMLLTNIAGLMDKQGQVLTGLSTEQVNELIA 244 IG G GE++NIN D AG +A ALKA++L+LLT+++G+ D QG+V+T L+ E + E+ A Sbjct: 174 IGTGREGETFNINGDTAAGAIAAALKADRLLLLTDVSGVKDAQGKVVTELTVENIEEMTA 233 Query: 245 DGTIYGGMLPKIRCALEAVQGGVTSAHIIDGRVPNAVLLEIFTDSGVGTLI 295 G I GGM+PK + A++GGV +A I+DGR PNA LLE+FT+ G G++I Sbjct: 234 AGVIAGGMIPKTETCVTAIRGGVRAAVILDGRAPNACLLELFTEHGAGSII 284 Lambda K H 0.318 0.138 0.381 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 274 Number of extensions: 11 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 301 Length of database: 287 Length adjustment: 26 Effective length of query: 275 Effective length of database: 261 Effective search space: 71775 Effective search space used: 71775 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
Align candidate 3606894 Dshi_0324 (acetylglutamate kinase (RefSeq))
to HMM TIGR00761 (argB: acetylglutamate kinase (EC 2.7.2.8))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00761.hmm # target sequence database: /tmp/gapView.7107.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00761 [M=231] Accession: TIGR00761 Description: argB: acetylglutamate kinase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-81 257.6 5.8 5.9e-81 257.4 5.8 1.1 1 lcl|FitnessBrowser__Dino:3606894 Dshi_0324 acetylglutamate kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3606894 Dshi_0324 acetylglutamate kinase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 257.4 5.8 5.9e-81 5.9e-81 2 231 .] 32 261 .. 31 261 .. 0.98 Alignments for each domain: == domain 1 score: 257.4 bits; conditional E-value: 5.9e-81 TIGR00761 2 iViKiGGaais..elleelakdiaklrkegiklvivHGGgpeinelleklgievefvnglRvTdketlevvemvlig 76 +ViK GG+a+ e++ ++a+di+ +r++g+++vivHGGgp+in++l kl+i+ +fvng RvTd++t+evvemvl g lcl|FitnessBrowser__Dino:3606894 32 VVIKFGGHAMGdaEAMASFARDIVLMRQVGVNPVIVHGGGPMINAMLAKLDINSDFVNGKRVTDAATIEVVEMVLSG 108 8*********9888999************************************************************ PP TIGR00761 77 kvnkelvallekhgikavGltgkDgqlltaekldkedlgyvGeikkvnkelleallkagiipviaslaldeegqllN 153 vnk++v++++++g +a+Gl+gkD++l++ + d + lg+vGe +v+++ l +l+ ++iipvia++++ eg+++N lcl|FitnessBrowser__Dino:3606894 109 LVNKRIVQAINREGGRAIGLSGKDANLIVCDPADPA-LGFVGEPVEVTPDTLLQLVRSEIIPVIAPIGTGREGETFN 184 ***********************************9.**************************************** PP TIGR00761 154 vnaDtaAaelAaaleAekLvlLtdvaGilegdkksliseleleeieqlikqavikgGmipKveaalealesgvkkvv 230 +n+DtaA+++Aaal+A++L+lLtdv+G+ + + ++++el++e+ie++ +vi+gGmipK e ++ a+++gv+++v lcl|FitnessBrowser__Dino:3606894 185 INGDTAAGAIAAALKADRLLLLTDVSGVKDA-QGKVVTELTVENIEEMTAAGVIAGGMIPKTETCVTAIRGGVRAAV 260 *******************************.666****************************************99 PP TIGR00761 231 i 231 i lcl|FitnessBrowser__Dino:3606894 261 I 261 8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (287 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 11.69 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory